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Squirrel command line tool manual

The squirrel command line tool is a front-end to the Squirrel data access infrastructure.

It offers functionality to

  • inspect various aspects of a data collection.

  • pre-scan / index file collections.

  • download data from online sources (FDSN web services, earthquake catalogs).

  • convert large data collections (file format and directory layout)

  • manage separate (isolated, local) environments for different projects.

  • manage persistent selections to speed up access to very large datasets.

Please read the Tutorial to get started with the squirrel command line tool.

Command reference

The squirrel tool and its subcommands are self-documenting with the --help option. Run squirrel without any options to get the list of available subcommands. Run squirrel SUBCOMMAND --help to get details about a specific subcommand, e.g. squirrel scan --help.

Common options

Options shared between subcommands are grouped into three categories:

  • General options include --loglevel to select the program’s verbosity and --progress to control how progress status is indicated. These are provided by all of Squirrel’s subcommands.

  • Data collection options control which files and other data sources should be aggregated to form a dataset. Use the --add option to add files and directories. Further options are available to include/exclude files by regular expression patterns, to restrict to use selected content kinds only (waveform, station, channel, response, event), to create persistent data selections and more. Finally, the --dataset option is provided to configure the dataset conveniently in a YAML file rather than repeatedly with the many command line options. Using --dataset includes the possibility to add online data sources.

  • Data query options are used to restrict processing/presentation to a subset of a data collection. They have no influence on the data collection itself, only on what is shown. It is possible to query by time interval (--tmin, --tmax, --time), channel/station code pattern (--codes), and content kinds (--kinds).

Examples

Renaming waveform channel codes

I have waveforms with channels named p0, p1 and p2. I would like to rename them to HHZ, HHN, and HHE, respectively:

squirrel jackseis --add data/old --out-sds-path data/new --rename-channel 'p0:HHZ,p1:HHN,p2:HHE'

This will create a new directory hierarchy in SDS layout under data/new with the modified waveforms.

For further possibilities, look for --rename-channel in the output of squirrel jackseis --help.

Set network code on a set of waveforms

I have waveforms where the network code is partially missing and partially incorrect. I would like to set it for all waveforms to XX:

squirrel jackseis --add data/old --out-sds-path data/new --rename-network XX

Convert raw waveforms to instrument-corrected ground velocity

I would like to convert raw waveforms to ground velocity in m/s. I have continuous waveforms and I don’t want to have any gaps in the output:

squirrel jackseis --add data/raw meta/stations.xml --out-sds-path data/velocity \
   --quantity velocity --band 0.1,10

This will restitute the seismograms to ground velocity in the frequency band 0.1 to 10 Hz. It uses pyrocko.trace.Trace.transfer() under the hood. The frequency taper involved is flat between 0.1 and 10 Hz and decays to zero at 0.1/2 and 10*2 Hz.

Reducing memory consumption when converting data with squirrel jackseis

Data is processed in time blocks matching the time increment given with --tinc (plus padding). All available data in the current block is loaded into memory. This may lead to excessive memory usage when lots of channels are available in the dataset.

Add --traversal sensor to process the dataset sensor by sensor. It will run a loop over time for each sensor in the dataset and thus use less memory.